Targeted RNA Sequencing for Gene Expression Analysis Using NGS

Fast and simple gene expression method with Ion AmpliSeq RNA panels

Comprised of targets selected from over 20,000 well annotated RefSeq genes, Ion AmpliSeq RNA panels help to empower high-throughput gene expression analysis with high sensitivity and specificity. Ion AmpliSeq RNA panels are straightforward to implement as they take advantage of the simple and fast sequencing workflow of the Ion S5 and Ion Chef Systems, offering a simpler and cost-effective alternative to whole transcriptome sequencing.

If you’re interested to learn about other Ion Torrent RNA solutions, we'll be sponsoring a webinar on November 14, 2017 about exosome miRNA sequencing for biomarker profiling (supported by Ion Total RNA-Seq). Please register below. You can also view an on-demand webinar to learn how to apply a targeted NGS gene expression–based approach in biomarker discovery.

Creating and ordering custom panels is easy with Ion AmpliSeq Designer—a free, online assay design tool that connects you directly to our assay design pipeline. Create and order custom RNA panels by simply selecting your targets of interest or entering your specific genomic content online, and we will design and create a customized Ion AmpliSeq panel just for you. Leveraging more than a decade of expertise powering the Applied Biosystems TaqMan Custom Assay design pipeline, the Ion AmpliSeq Designer tool produces optimized primer designs in as little as a few minutes. You now have the flexibility to analyze panels of genes of your choosing, such as those implicated in a particular disease state or representing specific biological pathways with anywhere from 12 to 1,200 human amplicons in a single reaction. Each design accounts for GC content, is filtered for repeats and SNPs, and selects target exons that represent the maximum number of transcripts for genes having multiple transcript isoforms documented in standard databases such as RefSeq.

Pre-designed customizable panels

Pre-designed Ion AmpliSeq panels have amplicon designs that have been evaluated through Ion AmpliSeq Transcriptome Human Gene Expression Panel. Their content includes gene lists curated from KOL publications and databases. They are customizable, so you can add or remove genes to update the amplicon list.

Panel content for our pre-designed panels is available on AmpliSeq.com to customize and order.

Ion AmpliSeq RNA Fusion Lung Cancer Research Panel

Developed with input from the OncoNetwork Consortium, the Ion AmpliSeq RNA Fusion Lung Cancer Research Panel was designed to detect expression imbalance in fusion driver genes using only 10 ng of FFPE RNA. The panel is a single pool of primers targeting fusion transcripts included in the ALK, RET, ROS1, and NTRK genes.

Data analysis with Torrent Suite Software and third party software (for more extensive analysis).

Torrent Suite Software coordinates all the experiment planning and data processing steps necessary to complete your targeted sequencing workflow. New product templates enable users to plan targeted runs simply and quickly. In just a few hours, raw data are captured on the Ion PGM or Ion S5 sequencer and transferred to the Torrent Server for base calling. Digital counting is then completed using the AmpliSeqRNA plug-in, which reports normalized transcript counts in spreadsheet file formats, enabling users to import data into other software packages for differential expression analysis.

Excellent correlation with TaqMan Assays

Universal human reference (UHR) RNA and human brain reference (HBR) RNA control samples were used to compare fold change for each of the 50 genes included in the Ion AmpliSeq RNA Cancer Research Panel against the fold change calculations of the same genes with TaqMan Gene Expression Assays. A resulting correlation of 0.989 was observed. These results show the accuracy of the gene expression data obtained with the Ion AmpliSeq RNA workflow.

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* Based on recommendations of multiplexing 4-6 libraries generated using the Ion AmpliSeq™ RNA Apoptosis Panel on one 318™ chip. **The content provided herein may relate to products that have not been officially released and is subject to change without notice.